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Yorodumi- EMDB-1657: Structural insight into nascent polypeptide chain-mediated transl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1657 | |||||||||
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Title | Structural insight into nascent polypeptide chain-mediated translational stalling | |||||||||
Map data | TnaC-stalled 70S Escherichia coli ribosome with P-site tRNA. | |||||||||
Sample |
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Keywords | TnaC / 70S ribosome / stalling | |||||||||
Function / homology | Function and homology information stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
Authors | Seidelt B / Innis CA / Wilson DN / Gartmann M / Armache J / Villa E / Trabuco LG / Becker T / Mielke T / Schulten K ...Seidelt B / Innis CA / Wilson DN / Gartmann M / Armache J / Villa E / Trabuco LG / Becker T / Mielke T / Schulten K / Steitz TA / Beckmann R | |||||||||
Citation | Journal: Science / Year: 2009 Title: Structural insight into nascent polypeptide chain-mediated translational stalling. Authors: Birgit Seidelt / C Axel Innis / Daniel N Wilson / Marco Gartmann / Jean-Paul Armache / Elizabeth Villa / Leonardo G Trabuco / Thomas Becker / Thorsten Mielke / Klaus Schulten / Thomas A ...Authors: Birgit Seidelt / C Axel Innis / Daniel N Wilson / Marco Gartmann / Jean-Paul Armache / Elizabeth Villa / Leonardo G Trabuco / Thomas Becker / Thorsten Mielke / Klaus Schulten / Thomas A Steitz / Roland Beckmann / Abstract: Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent ...Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a 5.8 angstrom-resolution cryo-electron microscopy and single-particle reconstruction of a ribosome stalled during translation of the tnaC leader gene. The nascent chain was extended within the exit tunnel, making contacts with ribosomal components at distinct sites. Upon stalling, two conserved residues within the peptidyltransferase center adopted conformations that preclude binding of release factors. We propose a model whereby interactions within the tunnel are relayed to the peptidyltransferase center to inhibit translation. Moreover, we show that nascent chains adopt distinct conformations within the ribosomal exit tunnel. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1657.map.gz | 5.2 MB | EMDB map data format | |
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Header (meta data) | emd-1657-v30.xml emd-1657.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | TnaC-Emdb.png | 309.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1657 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1657 | HTTPS FTP |
-Validation report
Summary document | emd_1657_validation.pdf.gz | 256.3 KB | Display | EMDB validaton report |
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Full document | emd_1657_full_validation.pdf.gz | 255.4 KB | Display | |
Data in XML | emd_1657_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1657 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1657 | HTTPS FTP |
-Related structure data
Related structure data | 4v5hMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1657.map.gz / Format: CCP4 / Size: 94.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TnaC-stalled 70S Escherichia coli ribosome with P-site tRNA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 1.23 Å / Y: 1.2375 Å / Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TnaC stalled 70S ribosome with P-site tRNA.
Entire | Name: TnaC stalled 70S ribosome with P-site tRNA. |
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Components |
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-Supramolecule #1000: TnaC stalled 70S ribosome with P-site tRNA.
Supramolecule | Name: TnaC stalled 70S ribosome with P-site tRNA. / type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: Monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 2.7 MDa |
-Supramolecule #1: 70S E. coli
Supramolecule | Name: 70S E. coli / type: complex / ID: 1 / Name.synonym: 70S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 2.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | Details: 50 mM Tris-HCl pH 8.0, 10 mM Mg-Acetate, 50 mM KCl, 10 mM NH4Cl, 2 mM EGTA, 2 mM L-tryptophan, 10 mM DTT |
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Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 95 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Number real images: 128 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 38900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: FEI Polara cartridge system / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Defocus group volumes |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 263000 |
-Atomic model buiding 1
Initial model | PDB ID: 3fih |
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Software | Name: MDFF |
Details | Protocol: MDFF |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-4v5h: |